Chemical approaches to understanding biological mechanisms

A report on work with small-molecule inhibitors of cellular processes presented at the 39th Annual Meeting of the American Society for Cell Bilogy, Washington DC, December 11-15, 1999     

Scanning the fossil record: stratophenomics and the generation of primary evolutionary-ecological data

The amount and quality of paleontological data is rapidly increasing thanks to the new developments in geological dating, 3D visualization and morphometrics, chemical and histological analysis, and database storage. However, despite the fact that data from fossils, their assemblages, temporal successions, spatial gradients and environments are of an evolutionary-ecological nature, their contribution to current mainstream evolutionary-ecological theory and methodology is low. The use of fossils is not seldom restricted to calibration (e.g., in phylogenetics), or source for historical speculation after having analyzed modern data first (e.g., in macroecology). Yet, the scale of resolution of many paleontological time series (10³–10⁵ years) is highly apt for studying the dynamics of species, the average lifetime of which is in the order of 10⁶–10⁷ years. In order to fully profit from the wealth of data from the rock archive, a large-scale “stratophenomics” approach is needed. The resulting data archives will not only further contribute to an increase in the knowledge of past species, communities and environments, but will also generate more and innovative theory on the mechanisms underlying species and higher taxon dynamics. Examples of new and promising approaches towards generating paleontological data will be presented under the headings of the three major stratophenomics dimensions: time, morphology and environment. Highlighted fields include astrochronology, sclerochronology and 3D morphometrics.     

Hominin cognitive evolution: identifying patterns and processes in the fossil and archaeological record

As only limited insight into behaviour is available from the archaeological record, much of our understanding of historical changes in human cognition is restricted to identifying changes in brain size and architecture. Using both absolute and residual brain size estimates, we show that hominin brain evolution was likely to be the result of a mix of processes; punctuated changes at approximately 100 kya, 1 Mya and 1.8 Mya are supplemented by gradual within-lineage changes in Homo erectus and Homo sapiens sensu lato. While brain size increase in Homo in Africa is a gradual process, migration of hominins into Eurasia is associated with step changes at approximately 400 kya and approximately 100 kya. We then demonstrate that periods of rapid change in hominin brain size are not temporally associated with changes in environmental unpredictability or with long-term palaeoclimate trends. Thus, we argue that commonly used global sea level or Indian Ocean dust palaeoclimate records provide little evidence for either the variability selection or aridity hypotheses explaining changes in hominin brain size. Brain size change at approximately 100 kya is coincident with demographic change and the appearance of fully modern language. However, gaps remain in our understanding of the external pressures driving encephalization, which will only be filled by novel applications of the fossil, palaeoclimatic and archaeological records.     

The fossil record of fish ontogenies: Insights into developmental patterns and processes

One of the properties of fossils is to provide unique ontogenies that have the potential to inform us of developmental patterns and processes in the past. Although fossilized ontogenies are fairly rare, size series of relatively complete specimens for more than 90 fish species have been documented in the literature. These fossilized ontogenies are known for most major phylogenetic groups of fishes and have a broad stratigraphic range extending from the Silurian to the Quaternary with a good representation during the Devonian. Classically, size series have been studied in terms of size and shape differences, where subsequently allometric changes were used as indicators of heterochronic changes in Paleozoic placoderms and sarcopterygians. Quantitative analyses of fossilized ontogenies of dipnoans have been interpreted in terms of morphological integration and fluctuating asymmetry. Recently, reconstructed sequences of ossification have been used to identify recurrent patterns of similar development in actinopterygians and sarcopterygians in order to infer phenotypic developmental modularity and saltatory pattern of development. Phylogenetic and temporal landmarks are put forward for some of the major developmental patterns in the evolution of fishes.     

Amphibian development in the fossil record

Ontogenetic series of extinct taxa are extremely rare and when preserved often incomplete and difficult to interpret. However, the fossil record of amphibians includes a number of well-preserved ontogenetic sequences for temnospondyl and lepospondyl taxa, which have provided valuable information about the development of these extinct groups. Here we summarize the current knowledge on fossil ontogenies of amphibians, their potential and limitations for relationship assessments, and discuss the insights they have provided for our understanding of the anatomy, life history, and ecology of extinct amphibians.     

Sex separation strategies: past experience and new approaches

The success of the sterile insect technique (SIT) and other genetic strategies designed to eliminate large populations of insects relies on the efficient inundative releases of competitive, sterile males into the natural habitat of the target species. As released sterile females do not contribute to the sterility in the field population, systems for the efficient mass production and separation of males from females are needed. For vector species like mosquitoes, in which only females bite and transmit diseases, the thorough removal of females before release while leaving males competent to mate is a stringent prerequisite. Biological, genetic and transgenic approaches have been developed that permit efficient male-female separation for some species considered for SIT. However, most sex separation methods have drawbacks and many of these methods are not directly transferable to mosquitoes. Unlike genetic and transgenic systems, biological methods that rely on sexually dimorphic characters, such as size or development rate, are subject to natural variation, requiring regular adjustment and re-calibration of the sorting systems used. The yield can be improved with the optimization of rearing, but the scale of mass production places practical limits on what is achievable, resulting in a poor rearing to output ratio. High throughput separation is best achieved with scalable genetic or transgenic approaches.     

Rates of speciation in the fossil record

Data from palaeontology and biodiversity suggest that the global biota should produce an average of three new species per year. However, the fossil record shows large variation around this mean. Rates of origination have declined through the Phanerozoic. This appears to have been largely a function of sorting among higher taxa (especially classes), which exhibit characteristic rates of speciation (and extinction) that differ among them by nearly an order of magnitude. Secular decline of origination rates is hardly constant, however; many positive deviations reflect accelerated speciation during rebounds from mass extinctions. There has also been general decline in rates of speciation within major taxa through their histories, although rates have tended to remain higher among members in tropical regions. Finally, pulses of speciation appear sometimes to be associated with climate change, although moderate oscillations of climate do not necessarily promote speciation despite forcing changes in species' geographical ranges.     

Patterns of heterochrony in the fossil record

Recent analyses of the fossil record have revealed that heterochrony has played a significant role in the evolution of most marine invertebrate groups. Recognition of several different heterochronic processes has allowed their influence under different ecological regimes to be assessed. Furthermore, recent research has demonstrated significant differences in frequencies of these processes between groups and at their different stages of phylogenetic development. The fossil record shows that heterochron y has been an important component in the generation of evolutionary trends. Heterochrony is an important factor in macroevolution because it can result in relatively abrupt morphological change with only minimum alteration of the genome.     

Using ghost lineages to identify diversification events in the fossil record

Observed rises in taxic diversity could reflect bias of the fossil record or a genuine diversification. Here we outline a new method that attempts to differentiate between these two possible explanations. The method is based on the calculations of average ghost lineage duration through successive intervals of time. Biases due to variation in preservational conditions affect taxa independently from their position in the tree of life. A genuine radiation event will affect some parts of the tree of life more than others. During periods of rapid diversification, there will be a high proportion of new taxa showing short ghost lineages and therefore the average ghost lineage duration will drop as diversity rises, allowing us to distinguish such events from preservational bias during which ghost lineage duration remains unchanged. We test the method on Aptian-Maastrichtian (Cretaceous) ray-finned fish diversity. The result shows that a peak of diversity in the Cenomanian is associated with a drop in average ghost lineage duration, indicating that a genuine biological radiation occurred at that time.     

Power spectra of extinction in the fossil record

Recent Fourier analyses of fossil extinction data have indicated that the power spectrum of extinction during the Phanerozoic may take the form of 1/f noise, a result which, it has been suggested, could be indicative of the presence of `critical dynamics'' in the processes giving rise to extinction. In this paper we examine extinction power spectra in some detail, using family-level data from two widely available compilations. We find that although the average form of the power spectrum roughly obeys the 1/f law, the spectrum can be represented more accurately by dividing it into two regimes: a low-frequency one which is well fit by an exponential, and a high-frequency one in which it follows a power law with a 1/f² form. We give explanations for the occurrence of each of these behaviours and for the position of the crossover between them.     

Patterns of generic extinction in the fossil record

Analysis of the stratigraphic records of 19,897 fossil genera indicates that most classes and orders show largely congruent rises and falls in extinction intensity throughout the Phanerozoic. Even an ecologically homogeneous sample of reef genera shows the same basic extinction profile. The most likely explanation for the congruence is that extinction is physically rather than biologically driven and that it is dominated by the effects of geographically widespread environmental perturbations influencing most habitats. Significant departures from the congruence are uncommon but important because they indicate physiological or habitat selectivity. The similarity of the extinction records of reef organisms and the marine biota as a whole confirms that reefs and other faunas are responding to the same history of environmental stress.     

Myxomycete diversity and distribution from the fossil record to the present

The myxomycetes (plasmodial slime molds or myxogastrids) are a group of eukaryotic microorganisms usually present and sometimes abundant in terrestrial ecosystems. Evidence from molecular studies suggests that the myxomycetes have a significant evolutionary history. However, due to the fragile nature of the fruiting body, fossil records of the group are exceedingly rare. Although most myxomycetes are thought to have very large distributional ranges and many species appear to be cosmopolitan or nearly so, results from recent studies have provided evidence that spatial distribution patterns of these organisms can be successfully related to (1) differences in climate and/or vegetation on a global scale and (2) the ecological differences that exist for particular habitats on a local scale. A detailed examination of the global distribution of four examples (Barbeyella minutissima, Ceratiomyxa morchella, Leocarpus fragilis and Protophysarum phloiogenum) demonstrates that these species have recognizable distribution patterns in spite of the theoretical ability of their spores to bridge continents. Special Issue: Protist diversity and geographic distribution. Guest editor: W. Foissner.     

Biomineralization: linking the fossil record to the production of high value functional materials

The microbial cell offers a highly efficient template for the formation of nanoparticles with interesting properties including high catalytic, magnetic and light-emitting activities. Thus biomineralization products are not only important in global biogeochemical cycles, but they also have considerable commercial potential, offering new methods for material synthesis that eliminate toxic organic solvents and minimize expensive high-temperature and pressure processing steps. In this review we describe a range of bacterial processes that can be harnessed to make precious metal catalysts from waste streams, ferrite spinels for biomedicine and catalysis, metal phosphates for environmental remediation and biomedical applications, and biogenic selenides for a range of optical devices. Recent molecular-scale studies have shown that the structure and properties of bionanominerals can be fine-tuned by subtle manipulations to the starting materials and to the genetic makeup of the cell. This review is dedicated to the late Terry Beveridge who contributed much to the field of biomineralization, and provided early models to rationalize the mechanisms of biomineral synthesis, including those of geological and commercial potential.     

The study of endocrine-disrupting compounds: past approaches and new directions

Over the last decade, evidence has mounted demonstrating thathuman-made compounds released into the environment are disruptingendocrine systems of animals. Research has centered largelyon direct steroidogenic or antisteroidogenic effects of thesecompounds with a recent focus on development of rapid in vitroassays employing estrogen receptors. A literature search andanalysis confirms attention placed on estrogen and anti-estrogen-likeaspects of endocrine disruption at the receptor level. Non-steroidalcomponents of the hypothalamic-pituitary-end gland axes havereceived much less attention in the published endocrine disruptionliterature. Furthermore, aspects of endocrine physiology, suchas the ability of animals to cope with stress or communicatechemically, have also received relatively less literature attentionwhen compared to disruption of development and reproduction.As researchers continue to investigate complex mixes of human-synthesizedcompounds in the environment, it is critical to broaden thespectrum of hormonal disruption investigated beyond estrogenicand androgenic actions and to determine how exposure to mixesaffects physiological function beyond reproduction. Last, inthe field of endocrine disruption, it also important to beginto use data on individuals for development of hypotheses regardingfitness risks, changes in population dynamics, and the potentialfor ecosystem level disruption.     

Modelling logistic growth by a new diffusion process: Application to biological systems

The present paper introduces a new diffusion process for the purpose of modelling logistic-type behaviour patterns. Unlike other processes in the same context, this one verifies that its mean function is a logistic curve. In addition, its transition density can be found explicitly, which allows to analyse inference from the discrete sampling of trajectories. The main features of the process will be analysed and the maximum likelihood estimation of parameters will be carried out through discrete sampling. Regarding the numerical problems found to solve the likelihood equations, several strategies are developed for obtaining initial solutions for the usual numerical procedures. Such strategies are compared by means of a simulation example. Also, another simulation study is carried out in order to compare the estimation in this process to that developed by means of continuous sampling in the logistic diffusion model considered by Giovanis and Skiadas (1999). Finally an example is given for the growth of a microorganism culture. This example illustrates the predictive possibilities of the new process, as well as its ability to study time variables formulated as first-passage-times.     

Climatic influences on species: Evidence from the fossil record

The detailed Neogene and Quaternary paleoclimatic reconstructions now available provide a means to test how species respond to environmental change. Paleontologic studies of marine organisms show that climatic change causes evolution (via cladogenesis and anagenesis), ecophenotypic variation, migration, morphologic stasis and extinction. Evolution during climatic change is a rare event relative to the number of climatic cycles that have occurred, but climate-related environmental barriers, usually temperature, may play an important role in the isolation of populations during allopatric speciation.